fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) (by OpenGene)
CHM13
The complete sequence of a human genome (by marbl)
| fastp | CHM13 | |
|---|---|---|
| 9 | 13 | |
| 1,775 | 865 | |
| 2.3% | 1.6% | |
| 4.7 | 4.9 | |
| 27 days ago | about 1 month ago | |
| C++ | ||
| MIT License | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
fastp
Posts with mentions or reviews of fastp.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-12-09.
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R pipelines for bulk RNA-seq analyses
fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
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NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
1) QC the data with fastp. This'll trim out adapters and toss reads that are poor quality.
- Illumina adapters and quality trimming
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Low-complexity sequence filtering tool
fastp has an adjustable low complexity filter option.
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Can you evaluate my pipeline?
- in terms of preprocessing and QC, I prefer fastp (https://github.com/OpenGene/fastp)
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Current QC tools for short read and long read sequencing
I generally use fastp as an all-in-one tool for short reads: https://github.com/OpenGene/fastp
- Qurstion about automating trimming process
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What methods (conda installable only please) can you use to determine the complexity of a fastq file? (e.g., kmer analysis)
I don't know if this fits exactly what you need, but I'm using fastp to check my fastq.gz files lately: https://github.com/OpenGene/fastp. You can install it via conda.
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A tool to count basepair in fastq file
If you also need some other basic statistics or want to filter the reads you can try fastp (https://github.com/OpenGene/fastp). If only the basepair count is needed, awk might be the fastest solution as suggested before.
CHM13
Posts with mentions or reviews of CHM13.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-09-14.
- VCF file for practice
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NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).
- The human Y chromosome has been sequenced
- The human genome is, at long last, complete
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The complete sequence of a human genome
Code https://github.com/marbl/CHM13
- Scientists publish the first complete human genome
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The first fully complete human genome with no gaps is now available to view for scientists and the public, marking a huge moment for human genetics. The six papers are all published in the journal Science.
Liftover files are already available from https://github.com/marbl/CHM13
- Why there is a lot of Ns at the begining of the fasta file of all Human chromosomes
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The Entire Human Genome Has Been Sequenced
If you’re serious, you can download the current fasta file from this page.
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Digital Karyogram Derived From The Telomere-to-Telomere Consortium's CHM13/v1.1 Genome Assembly [OC]
I have created a simulated karyogram based on REPAVER visualisations of the Telomere-to-telomere Consortium's CHM13 assembly:
What are some alternatives?
When comparing fastp and CHM13 you can also consider the following projects:
galaxy - Data intensive science for everyone.
bowtie2 - A fast and sensitive gapped read aligner
readfq - A simple tool to calculate reads number and total base count in FASTQ file
glslSmartDeNoise - Fast glsl deNoise spatial filter, with circular gaussian kernel, full configurable
nextclade - Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
readfq - Fast multi-line FASTA/Q reader in several programming languages
seqtk - Toolkit for processing sequences in FASTA/Q formats
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
Sniffles - Structural variation caller using third generation sequencing
kraken2 - The second version of the Kraken taxonomic sequence classification system
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files